Biology subjects

Deshmukh, R.

Publications and source records attributed to Deshmukh, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Neurodegeneration risk variants promote lysosomal TMEM106B fibrilaccumulation

Variants in TMEM106B and GRN, which encode lysosomal proteins, interact through unknown mechanisms to increase the risk of age-related cognitive decline and neurodegeneration. Here, we show that these variants converge on a single molecular intermediate: the cleaved intra-lysosomal fibril core of TMEM106B, a precursor to amyloid fibrils that accumulate in the aging brain. A protein-coding TMEM106B risk variant (p.T185) drives fibril core accumulation by impairing its degradation and GRN risk variants amplify this effect. Mice over-expressing the fibril core develop hallmarks of neurodegeneration, and cryo-electron tomography reveals intra-lysosomal fibrils in cultured neurons, mice, and diseased human brain. In GRN-mutation carriers, in whom fibril burden is greatest, fibrils extrude through ruptured lysosomal membranes. These findings identify intra-lysosomal TMEM106B fibrillization as a convergent neurodegeneration mechanism and potential therapeutic target.

cell biology↗

bioRxiv2026

L-pentahomoserine correlates with therapy outcome in esophageal cancer and promotes metabolic adaptations that support cell survival under nutrient-deprived conditions

Esophageal adenocarcinoma (EAC) is the sixth-leading cause of cancer-related death. Although pyrimidine analogue-based neoadjuvant and adjuvant therapies are widely used, patient responses remain variable. Emerging evidence indicates that bacteria-derived metabolites influence tumor biology and therapy outcomes. To identify non-canonical plasma metabolites linked to cancer biology, we performed correlation analyses between untargeted metabolomics profiles and overall survival. This approach revealed a bacterial metabolite called L-pentahomoserine, or L-2-amino-5-hydroxypentanoic acid (L-2A5HPA), to be positively associated with overall survival. Notably, L-2A5HPA promoted cell survival under nutrient limitation by redirecting glucose metabolism towards aspartate and pyrimidine biosynthesis. In vitro, L-2A5HPA uptake varied among cell lines and was controlled by stereospecific transporters. Furthermore, metabolic profiling in mouse models of liver cancer showed different levels of L-2A5HPA and a strong correlation with pyrimidine intermediates, dihydroorotate and orotate. The link between L-2A5HPA, pyrimidine nucleotide metabolism, and cell survival provides mechanistic insight into its association with patient outcome. Our findings position L-2A5HPA as a metabolite with potential to become a prognostic biomarker for EAC and underscores its role in metabolic adaptation under nutrient-deprived conditions.

cancer biology↗

bioRxiv2026

Anxiety Selectively Impairs Reward Learning Under Uncertainty, While N3 Sleep Recalibrates It

Adapting to uncertain environments requires distinguishing stochastic variability from genuine environmental change, yet how anxiety and sleep shape this process remains unclear. Using a probabilistic reversal-learning task that simultaneously manipulated stochasticity and volatility, we show that high trait anxiety selectively impairs reward learning in stable but noisy environments, despite preserved sensitivity to true volatility. Computational modeling revealed that anxious individuals misattribute stochastic fluctuations to environmental change, resulting in elevated reward learning rates and impaired evidence accumulation. In a second experiment combining task performance with overnight sleep EEG, greater N3 sleep was associated with reduced learning rates and improved evidence accumulation. These findings identify a selective computational mechanism underlying anxiety-related learning deficits and suggest N3 sleep as a state-dependent pathway for recalibrating adaptive learning under uncertainty.

neuroscience↗

bioRxiv2025

Oxidative-stress related increase in keratoconus tear MDA and GPX3 while NRF2-antioxidant functions decrease in stromal cells

Keratoconus (KC) is a common eye disease where the cornea undergoes degenerative thinning and steepening. The absence of biomarkers for early diagnosis prior to the onset of overt corneal phenotypes and the lack of curative treatments rooted in a fundamental understanding of KC biology remain significant challenges. To address these issues, we investigated the role of unresolved oxidative stress in KC pathogenesis. Malondialdehyde (MDA) a lipid peroxidation byproduct that accumulates during oxidative stress was significantly elevated in the tears of KC patients compared to unaffected controls and positively correlated with maximal keratometry (Kmax), a measure of KC severity. Similarly, the secreted antioxidant glutathione peroxidase 3 (GPX3), was significantly increased in patient tears, and strongly correlated with Kmax. In a cell culture model of oxidative stress, KC corneal stromal cells displayed increased apoptosis and suboptimal activation of NRF2, a transcription factor master regulator of antioxidant genes. Conversely, inhibition of NRF2 in donor stromal cells elicited KC-like cellular phenotype, whereas sulforaphane, an NRF2 booster restored antioxidant gene expression and the deposition of cornea-typical collagens. Our study identified cellular antioxidant signaling dysregulations in keratoconus where sulforaphane treatment may be restorative. Consistent increases in patient tear MDA and GPX3 present these as promising biomarkers for KC diagnosis and severity predictions.

cell biology↗

bioRxiv2025

Transcriptomes of higher order thalamic nuclei in obsessive compulsive disorder

Obsessive-compulsive disorder (OCD) is a chronic psychiatric illness associated with altered function in cortico-striatal-thalamo-cortical (CSTC) circuits. In this pilot study, we examined differential RNA expression in the thalamus using postmortem human brain tissue samples from 11 subjects with OCD and 10 unaffected subjects. We individually dissected the mediodorsal magnocellular, mediodorsal parvocellular, and ventral anterior nuclei, which participate in orbitofrontal and anterior cingulate CSTC circuits most frequently associated with OCD, and the posterior ventrolateral nucleus, which participates in premotor and motor circuits that are increasingly implicated in OCD. Preselected GABAergic, glutamatergic and ion channel genes were analyzed via qPCR. Two genes required for GABA synthesis and release, GAD1 and SLC32A1, were found to be downregulated in OCD subjects across all nuclei, and potassium channel KCNN3 was upregulated. In parallel, we performed an exploratory total RNAseq differential expression analysis. We identified few (12 - 52) differentially expressed genes (DEGs) in each nucleus, and only one DEG in a pooled analysis of all nuclei. No DEGs were significant after correction for multiple comparisons. Investigation by model selection indicated that OCD diagnosis was not a useful factor in modelling gene expression in our dataset. OCD was also not associated with any modules of co-expressed genes identified using weighted gene correlation network analysis. Overall, we found minimal evidence of differential RNA expression in these thalamic nuclei in OCD. These findings contrast with our previous work including many of the same subjects where we found widespread differential mRNA expression in the orbitofrontal cortex and striatum in OCD.

neuroscience↗

bioRxiv2025

Increased mRNA translation delays lung adenocarcinoma initiation and exposes a therapeutic vulnerability to MEK inhibitors

Although protein synthesis inhibitors are being evaluated as anti-cancer agents, the dynamics of mRNA translation in early tumorigenesis are still poorly understood. We report that deletion of the mRNA-translation repressor, eIF4A2 in early KRAS-driven lung adenocarcinoma leads to a dysregulated protein synthesis landscape characterised by a strongly upregulated secretome, enlarged secretory compartments, increased oxidative metabolism and acquisition of senescence-like characteristics. Paradoxically, this overdriven protein synthesis landscape delays tumorigenesis and leads to appearance of clusters of non-proliferative, p21-positive KRAS-expressing cells in the lung. Administration of rapamycin to reduce mRNA translation suppresses senescence and restores tumorigenesis following eIF4A2 deletion. Importantly, some eIF4A2 knockout cells overcome senescence to form tumours that exhibit enhanced MAP-kinase signalling and, in contrast to eIF4A2+/+ lesions, these may be eradicated by administration of a MEK inhibitor. Thus, dysregulated mRNA translation exposes a potential therapeutic vulnerability in KRAS-driven lung adenocarcinoma by forcing cancer cells to rely on MEK signalling. Statement of significanceThe requirement for anabolism in cancers has led to the search for inhibitors of mRNA translation as anti-cancer agents. However, we report that increased rates of mRNA translation promote a senescence-like phenotype in KRAS-driven lung cancer which delays tumorigenesis and renders the resulting tumours sensitive to MEK inhibition.

cancer biology↗

bioRxiv2024

Maternal Med12 safeguards trophoblast pluripotency and placental development

For a brief but critical period post-fertilization, the mammalian embryo is entirely dependent on maternal products inherited from the oocyte. Previous research showed that oocyte-specific loss of Med12, an X-linked gene and Mediator complex subunit, leads to female sterility despite normal folliculogenesis and ovulation. Here, we show that loss of maternal Med12 has minimal effect on the oocyte transcriptome and does not manifest in embryonic lethality until post-implantation. Implants derived from Med12-null oocytes demonstrate abnormal placentation at E9.5, with an overabundance of trophoblast giant cells (TGC). This phenotype associates with downregulation of trophoblast pluripotency markers (e.g. Cdx2) and activation of drivers of TGC identity (e.g. Stra13) in the E7.5 extraembryonic ectoderm, revealing a previously undescribed role for Med12 in trophoblast pluripotency maintenance. Notably, we find consistently low Med12 expression in embryos derived from Med12-null oocytes, potentially due to programmed paternal X chromosome inactivation (XCI). To isolate the consequences of maternal Med12 depletion, we introduced an autosomal Med12 transgene and show that embryonic expression of the transgene rescues development of Med12-null oocytes. We conclude that oocyte-specific deletion of Med12 produces a maternal-zygotic double knock-out in extraembryonic tissues due to paternal XCI, leading to loss of pluripotency in the trophoblast, placental malformation, and embryonic death.

developmental biology↗

bioRxiv2024

The loss of a supergene in obligately polygynous Formica wood ant species

Some of the most striking examples of phenotypic variation within species are controlled by supergenes. However, most research on supergenes has focused on their emergence and long-term maintenance, leaving the later stages of their life cycle largely unexplored. Specifically, what happens to a derived supergene haplotype when the trait it controls reaches fixation? Here we answer this question using the ancient supergene system of Formica ants, where (monogynous) single-queen colonies carry only the ancestral haplotype M while the derived haplotype P is exclusive to (polygynous) colonies with multiple queens. Through comparative genomics of all seven European wood ant species, we found that the P haplotype was present in only one of the three obligate polygynous species (F. polyctena). In the two others (F. aquilonia and F. paralugubris) the P haplotype was completely missing except for duplicated P-specific paralogs of two genes, Zasp52 and TTLL2, with Zasp52 being directly involved in wing muscle development. We hypothesize that these genes play a direct role in polygyny and contribute to differences in body size and/or dispersal behaviour between monogynous and polygynous queens. A complete lack of P/P genotypes among the 136 workers suggest strong selection against such genotypes. While our analyses did not reveal evidence of increased mutation load on the P, it is possible that this skew in genotype distributions is driven by a few loci with strong fitness effects. We propose that selection to escape P-associated fitness costs underlies the loss of this haplotype in obligate polygynous wood ants.

genomics↗

bioRxiv2024

Evolution of novel mimicry polymorphisms through Haldanes sieve and rare recombination

Origins of phenotypic novelty represent a paradox. Maintenance of distinct, canalized morphs usually requires a complex array of polymorphisms, whose co-retention requires a genetic architecture resistant to recombination, involving inversions and master regulators. Here, we reveal how such a constraining architecture can still accommodate novel morphs in evolving polymorphisms using the classic polymorphic Batesian mimicry in Papilio polytes, whose supergene-like genetic architecture is maintained in a large inversion. We show that rapidly evolving alleles of the conserved gene, doublesex, within this inversion underlie the genetic basis of this polymorphism. Using precisely dated phylogeny and breeding experiments, we show that novel adaptive mimetic morphs and underlying alleles evolved in a sequentially dominant manner, undergoing selective sweeps in the mimetic species as predicted under Haldanes sieve. Furthermore, we discovered that mimetic forms share precise inversion breakpoints, allowing rare exon swaps between the universally dominant and a recessive allele to produce a novel, persistent intermediate phenotype, ultimately facilitating the acquisition of phenotypic novelty. Thus, genetic dominance, selective sweeps, rapid molecular divergence, and rare recombination promote novel forms in this iconic evolving polymorphism, resolving the paradox of phenotypic novelty arising even in highly constrained genetic architectures.

evolutionary biology↗

bioRxiv2024

Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing

In agriculture, mineral nutrients uptake and deposition profoundly influence plant development, stress resilience, and productivity. Despite its classification as a non-essential element, silicon (Si) is crucial in plant physiology, particularly in defense response and stress mitigation. While genetic and molecular mechanisms of Si uptake and transport are well-studied in monocots, particularly rice, its role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. Traditional bulk transcriptomics methods lack the resolution to uncover cellular heterogeneity. Here, we present a study by utilizing single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. Our analysis revealed distinct cellular populations, including a novel Si-induced cell cluster within vascular cells, suggesting a specific mechanism of Si distribution. Si treatment induced the expression of defense-related genes, particularly enriched in vascular cells, highlighting their specialized role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in RNA silencing, phytoalexin biosynthesis, and immune receptor signaling, suggesting a mechanism of transcriptional priming of genes involved in defense responses. We further investigated putative Si transporters, revealing differential expression patterns in response to Si treatment, suggesting presence of active and gradient-based transport mechanisms. Our findings shed light on the vital biotic stress regulatory networks governed by Si treatment in soybean leaves, paving potential strategies for enhancing stress tolerance and agronomic performance in crops.

plant biology↗

bioRxiv2024

Primary auditory cortex is necessary for the acquisition and expression of categorical behavior

The primary auditory cortex (ACtx) is critically involved in the association of sensory information with specific behavioral outcomes. Such sensory-guided behaviors are necessarily brain-wide endeavors, requiring a plethora of distinct brain areas, including those that are involved in aspects of decision making, motor planning, motor initiation, and reward prediction. ACtx comprises a number of distinct excitatory cell-types that allow for the brain-wide propagation of behaviorally-relevant sensory information. Exactly how ACtx involvement changes as a function of learning, as well as the functional role of distinct excitatory cell-types is unclear. Here, we addressed these questions by designing a two-choice auditory task in which water-restricted, head-fixed mice were trained to categorize the temporal rate of a sinusoidal amplitude modulated (sAM) noise burst and used transient cell-type specific optogenetics to probe ACtx necessity across the duration of learning. Our data demonstrate that ACtx is necessary for the ability to categorize the rate of sAM noise, and this necessity remains stable across learning. ACtx silencing substantially altered the behavioral strategies used to solve the task by introducing a fluctuating choice bias and increasing dependence on prior decisions. Furthermore, ACtx silencing did not impact the animals motor report, suggesting that ACtx is necessary for the conversion of sensation to action. Targeted inhibition of both intratelencephalic and extratelencephalic projections on just 20% of trials had a modest effect on task performance, but significantly degraded learning. Taken together, our data shows that ACtx plays a critical role in both the acquisition and expression of categorical behavior, and that distinct excitatory projections play important roles in learning and plasticity.

neuroscience↗

bioRxiv2023

Unravelling Silicon's Transcriptomic Armor in Soybean against Macrophomina phaseolina causing Charcoal Rot Disease

The Glycine max L. has been affected by more than 100 diseases, including Macrophomina phaseolina producing charcoal rot disease, which reduces production by 70%. In this investigation, RNA-Seq analysis is used for the first time to explore role of silicon in preventing soybean charcoal rot. The study explores the molecular mechanism underlying soybeans resilience to charcoal rot when treated with potassium silicon. It was meticulously investigated how Macrophomina phaseolina entered the roots. The SEM, which showed a strong link between potassium silicate accumulation and disease resistance. Further investigation indicates that a potassium silicate concentration of 1.7mM lowers disease incidence. Using Illumina HiSeq NGS data, we present a transcriptome analysis revealing genes associated with charcoal rot resistance, highlighting 3,106 genes with distinct expression patterns. The strong enrichment of pathways including "Biosynthesis of ansamycins" and "Flavone and flavonol biosynthesis," which contribute to resistance against charcoal rot, is highlighted by KEGG enrichment analysis. The ERF transcription factor and NB leucine-rich repeats stands out among the differentially expressed genes as being particularly connected to resistance. The crucial functions that many other important transcription factors, including as MYB, NAC, and proteins from the FAR1 family, play in enhancing soybeans resistance to charcoal rot are also noted. This newly discovered information could help in developing tactics to strengthen soybeans resistance to Macrophomina phaseolina.

microbiology↗

bioRxiv2023

Paracrine secretion of MUFAs prevents ferroptosis in triple-negative breast cancer and reveals selenocysteine synthesis dependency for lung metastasis

The limited availability of therapeutic options for patients with triple-negative breast cancer (TNBC) contributes to the high rate of metastatic recurrence and poor prognosis. Ferroptosis is a type of cell death caused by iron-dependent lipid peroxidation and counteracted by the antioxidant activity of the selenoprotein GPX4. Here, we show that TNBC cells secrete an anti-ferroptotic factor in the extracellular environment when cultured at high cell densities but are primed to ferroptosis when forming colonies at low density. We found that secretion of the anti-ferroptotic factors, identified as monounsaturated fatty acid (MUFA) containing lipids, and the vulnerability to ferroptosis of single cells depends on the low expression of stearyl-CoA desaturase (SCD) that is proportional to cell density. Finally, we show that the inhibition of Sec-tRNAsec biosynthesis, an essential step for selenoprotein production, causes ferroptosis and impairs the lung seeding of circulating TNBC cells that are no longer protected by the MUFA-rich environment of the primary tumour.

cancer biology↗

bioRxiv2022

Duplication and sub-functionalisation characterise diversification of opsin genes in the Lepidoptera

Gene duplication is a vital process for evolutionary innovation. Functional diversification of duplicated genes is best explored in multicopy gene families such as histones, hemoglobin, and opsins. Rhodopsins are photo-sensitive proteins that respond to different wavelengths of light and contribute to diverse visual adaptations across insects. While there are several instances of gene duplications in opsin lineages, the functional diversification of duplicated copies and their ecological significance is properly characterised only in a few insect groups. We examined molecular and structural evolution that underlies diversification and sub-functionalisation of four opsin genes and their duplicated copies across 132 species of the diverse insect order--Lepidoptera. Opsins have largely evolved under purifying selection with few residues showing signs of episodic and pervasive diversifying selection. Although these do not affect overall protein structures of opsins, substitutions in key amino acids in the chromophore-binding pocket of duplicated copies might cause spectral sensitivity shifts leading to sub-functionalisation or neofunctionalisation. Duplicated copies of opsins also exhibit developmental stage-specific expression in Papilio polytes, suggesting functional partitioning during development. Together, altered spectral sensitivities owing to key substitutions and differential expression of duplicated copies across developmental stages might enable enhanced colour perception and improved discrimination across wavelengths in this highly visual insect group.

evolutionary biology↗

bioRxiv2022

Reproductive barriers and genomic hotspots of adaptation during allopatric species divergence

Theory predicts that in allopatric populations, genomic divergence and reproductive barriers will be driven largely by random genetic drift, and thereby evolve slowly in large populations. However, local adaptation and divergence under selection may also play important roles, which remain poorly characterised. Here we address three key questions in young allopatric species: (a) How widespread are genomic signatures of adaptive divergence?, (b) What is the functional space along which young sister species show divergence at the genomic level?, and (c) How quickly might prezygotic and postzygotic reproductive barriers evolve? Analysis of 82 re-sequenced genomes of the Oriental Papilio polytes species group revealed surprisingly widespread hotspots of intense selection and selective sweeps at hundreds of genes unique to each species, and spanning all chromosomes, rather than divergence only in a few genomic islands. These genes perform diverse ecologically important adaptive functions such as wing development, colour patterning, courtship behaviour, mimicry, pheromone synthesis and olfaction, and host plant use and digestion of secondary metabolites, that could contribute to local adaptation and subsequent reproductive isolation. Divergence at such functional genes appeared to have reproductive consequences: behavioural and hybridisation experiments revealed strong assortative mate preference (prezygotic barriers) as well as postzygotic barriers to hybridisation in timespans as short as 1.27 my, indicating that speciation was already complete, rather than incipient. Our study thus demonstrates an underappreciated role of intense selection and potential local adaptation in creating genome-wide hotspots of rapid molecular evolution and divergence, during differentiation and speciation in young allopatric species.

evolutionary biology↗

bioRxiv2021

A kiwellin protein-like fold containing rust effector protein localizes to chloroplast and suppress cell death in plants

The effector proteins expressed by plant pathogens are one of the essential components of the host-pathogen interaction. Despite being important, most of the effector proteins remain unexplored due to the lack of conserved features and huge diversity in their primary sequence. In the present study, extensive secretome analysis was performed in sixteen major plant fungal pathogens to find the conserved features in the candidate secretory effector proteins (CSEPs) using homology and ab initio modeling approaches. Interestingly, a variable number of plant kiwellin proteins fold like secretory proteins were found in all the major rust fungal pathogens. Many of them are predicted as potential effector proteins. For instance, 26 out of 35 Kiwellin like proteins identified in Puccinia striiformis race 104E 137A were predicted as potential effector proteins. In addition, a kiwellin predicted effector gene, Pst_13960, from the Indian Puccinia striiformis race Yr9 was characterized using overexpression, localization, and deletion studies in Nicotiana benthamiana. The Pst_13960 suppressed the BAX-induced cell death and localized in the chloroplast. Furthermore, the expression of the kiwellin matching region (Pst_13960_kiwi) alone suppressed the BAX-induced cell death in N. benthamiana despite the change of location to the cytoplasm and nucleus, suggesting the novel function of the kiwellin fold in rust fungi. Further analysis of these proteins predicted these candidates to contain N-terminal Intrinsically disordered regions (IDRs) putatively associated with chloroplast translocation as deletion of region abolished the chloroplast localization of Pstr_13960. Overall, the current study reports the presence of kiwellin like proteins in rust fungi that act as a novel effector in plants. Author SummaryRust fungi are one of the most devastating plants infecting pathogens. These pathogens secrete several distinct proteins like effector proteins that help the pathogens in the establishment of infection by suppressing cell death induced by the plants. Despite being important, these effector proteins remain unexplored due to the lack of conserved features. Currently, different methods are being used to characterize them however, could not describe their specific function fully due to a lack of knowledge of the functional domain. Recent advancement in effector protein tertiary structure characterization using NMR (Nuclear magnetic resonance) and X-ray crystallography has been very helpful in identifying the conserved structural features defining functionality. However, these techniques are quite complicated and may take a lot of time and labor. On the other hand, the computational approaches for structural prediction of the effectors may help to identify known folds or domains with few efforts but at a significant level. Therefore, such computational approaches can be efficiently implemented in the preliminary screening of the candidates. In the present study using the computational structure prediction method, we were able to find several conserved novel kiwellin folds containing effectors, in different rust fungi. We characterized one of the candidates and it showed interference with artificially induced cell death in plants. This study highlights the novel function of the kiwellin like effector proteins of the rust fungi that are already identified to play a role in host defense against plant pathogens.

microbiology↗

bioRxiv2021

Comparative secretomics identifies conserved WAxR motif-containing effectors in rust fungi that suppress cell death in plants

Identification of novel effectors with conserved features has always remained a challenge in plant-pathogen interaction studies. The introduction of the genomics era in plant-pathogen studies has led to the identification of significant candidate effectors with novel motifs such as RxLR and dEER motifs. However, in the case of fungal pathogens, limited conserved motifs associated with effectors have been discovered yet. In the present study, we have performed comparative secretome analysis for major plant pathogens of diverse nutrition mechanisms with the aim of dissecting the features underlying their corresponding secretome and conserved motifs. We showed that rust fungi possess the lowest Cell wall degrading enzymes (CWDEs) consortium lower than other biotrophic pathogens. We also showed rust fungi possess the highest secretory superoxide dismutase (SOD) than other studied plant pathogens. Further, we prioritized the candidate secretory effectors proteins (CSEPs) of all the studied pathogens by combining various effector mining parameters to highlight the candidates with potential effector features. A novel WAxR motif in conjugation with the Y/F/WxC (FGC) motif was identified in the effectors of various P. striiformis races present globally. The WAxR/WAxR like motifs ( WxxR, WAxx, xAxR) containing effectors were also found in the secretome of other rust fungi. Further, the functional validation of two candidate effectors with WAxR motif from P. striiformis Yr9 showed that these effectors localize to the nucleus as well as cytoplasm, and are able to suppress BAX induced cell death in Nicotiana benthamiana. The mutation analysis of individual residues of the WAxR motif (W, A, R) however did not affect the cell death suppression nor subcellular localization of these effectors. Overall, the current study reports the presence of novel motifs in large numbers of effectors of rust fungi with cell death suppression features. HighlightsO_LISecretome analysis of various plant pathogens performed C_LIO_LIA prioritization list for candidate effectors designed C_LIO_LIA novel WAxR motif was discovered in rust fungal effector proteins C_LIO_LITwo WAxR candidate effectors were functionally validated C_LI

microbiology↗

bioRxiv2021

Horizontal transfer of a conserved npc-2 like effector gene in rust fungi that suppresses cell death in plants

ML/MD-2 is a conserved lipid/sterol-binding protein family having a role in sterol transfer and innate immunity in lower and higher eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 25 fungal and five oomycetes plant pathogen, having a different nutrition mode. All the fungal species were found to have varied numbers of family members, a distinctively substantial expansion of the ML gene family was observed in Rhizophagus irregularis (RI) with 33 genes. Our analysis also showed that NPC2 like proteins, a subfamily of ML domain superfamily, were not only restricted to animals and insect species but also present in plant fungal pathogens, including members of Clavicipitaceae, Pucciniacease, and Tremellaceae family. The phylogenetic analysis showed that these NPC2 like fungal proteins are more closely related to animals/insects than other fungal species. The molecular docking studies of these proteins with cholesterol and other derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. Further, the full length CDS of one of the npc2 like genes from Puccinia triticina (Pt5643) was PCR amplified and further characterized using various studies such as qRT-PCR, expression in onion epidermal cells, Nicotiana benthamiana for subcellular localization studies, yeast functional complementation, and expression studies. The mRNA abundance of Pt5643 was observed to be increased along with the infection progression and exhibits the highest expression at 5thday post-infection (dpi), suggesting its important role in the P. triticina infection cycle in wheat. The fluorescent confocal microscopy of transiently expressed YFP tagged Pt5643 in onion epidermal cells and N. benthamiana shows its location in cytoplasm and nucleus, indicating its involvement in the manipulation of host genes. The functional complementation of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic npc2 gene. Further, the overexpression of Pt5643 also suppressed the BAX and H2O2 induced program cell death in N. benthamiana and yeast, respectively thus proving to be a novel horizontally transferred effector in rust fungal pathogens. Altogether the present study reports the novel function of fungal NPC2 like proteins playing a crucial role in host defense manipulation possibly through lipid binding/transport similar to animals.

microbiology↗